MolNFT v1 · #125020 · protein
Crystal structure of extracellular domain of HER2 in complex with fcab H10-03-6
5KWG · Receptor tyrosine-protein kinase erbb-2: “Crystal structure of extracellular domain of HER2 in complex with fcab H10-03-6”. X-ray diffraction, 11 pockets (best druggability 0.84). MolNFT v1 #125020 on GenesisL1: 3D structure…
- PDB
- 5KWG
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; Ig gamma-1 chain C region
- EC
- 2.7.10.1
- UniProt
- P04626, P01857
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 561 | 8% helix, 18% strand | P04626 |
| A | Ig gamma-1 chain C region | protein | 212 | 9% helix, 32% strand | P01857 |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.84 | 0.94 | 58 | empty |
| 2 | 243 | 0.83 | 0.94 | 38 | empty |
| 3 | 56 | 0.65 | 0.93 | 18 | empty |
| 4 | 126 | 0.64 | 0.87 | 27 | empty |
| 5 | 479 | 0.63 | 0.76 | 54 | empty |
Interfaces
1 interface between chains.
- C–A · 585 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5KWG · Crystal structure of extracellular domain of HER2 in complex with Fcab H10-03-6 · the same entry in another collection · chain C against C, TM-score 1.00
- P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain C against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04626
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 5KWG · PDBe 5KWG · UniProt P04626 · UniProt P01857
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